Neon Exodus Yamato
by Classic Cowboy
Summary: fusion/inspired by Space Battleship Yamato. Years after Third Impact, 1/3 of mankind has risen from the Sea of LCL, but the fragile Earth is close to dying. A group of survivors of NERV, together on a space battleship built from the remains of a WWII relic, travel to where the Seeds of Life originated in a final hope of finding a way to save their world and mankind...
1. Chapter 1

_Millennia ago, the Ancestral Race from the far distant world of Iscandar launched the Seeds of Life throughout the galaxies. Two Seeds landed upon the 3__rd__ planet of the Sol System. The first to land contained the being that came to be known as the Angel Lilith, It wiped out a large number of life forms upon the planet, the First Impact, and she produced the Lilin, later known as Humanity. Unfortunately, a rare occurrence happened, and a second Seed of Life landed upon the planet Earth, this one containing the Angel Adam. Thousands of years passed by and the Lilin grew into a great race of nations, until they discovered the dormant second Seed of Life. Adam was awakened and the Second Impact began._

_War broke out against the Children of Adam and the Children of Lilith, while some foolishly sought to ascend to another plane of existence. Under the guise of creating defenders to battle the Children of Adam, hybrid creations called Evangelions were produced, with the bodies of Children of Adam, but with the souls of Lilin, and piloted by human children connected to the souls bound to the Evas, a long conflict broke out between them. Among them was a youth named Shinji Ikari. Tormented by his father and those working for him from a young age he was reared to bring about the end of the world and the rise of Instrumentality. Through interaction by his fellow Eva Pilots and those around him, at the last moment, at the peak of the Third Impact, he saved the Lilin. One Third of the Human race rose from the result of the Final Impact, but the world was devastated. Oceans were either evaporated or replaced by primordial fluid known as LCL, cities were leveled, and plant and animal life were wiped out._

_Six years has passed since Third Impact. Life on Earth is wearing thin and hope of survival fades by the day. But a new hope will soon rise from a relic of the past, manned by those who wish to redeem their actions…_

_**NEON EXODUS YAMATO **_

"Seagull to Tokyo-4, Seagull to Tokyo-4. Supply pick up of food and distilled water from Hong Kong has fully loaded and we are in the air and in route. We will be arriving in ETA two to three hours, if all well. Over."

"Tokyo-4 Acknowledge and will have the welcome wagon out for you, Seagull, fly safe."

"Roger that, T-4, Seagull out." Toji Suzuhara put the radio microphone back in its place and glanced to his partner in the pilot seat of their air transport _Seagull_. "Well back to Japan, huh?"

"Haven't been to Tokyo-4 in a few years," Shinji Ikari shook his head, "I might make it a few hours without a tomato thrown at my face."

"Tomatoes are in rare supply, my brother!" Toji laughed as he leaned back, "They won't waste one on you."

Shinji gave him a small smile. They had been friends since his time on Tokyo-3, before the Impact. Toji was one of the few who came back after he halted the Impact to not reject him angrily. After a few years of traveling on his own, Shinji stumbled across his old friend again, and for the last two years they had transported supplies across the devastated wasteland that was once the beautiful Planet Earth.

"This is weird," Toji said, bringing Shinji out of his thoughts.

"What's wrong?" Shinji asked, noticing his friend, who was studying a long range radar.

"A lot of air transports are moving toward Tokyo-4," Toji said, pointing to the various dots and their projected trajectories. "We got a pretty packed load, too. Something's up."

"Whatever it is, we may find out when we get there," Shinji said, glancing back to the window.

"Right, right," Toji nodded, unsnapping his restraint belts, "I'm going to check the load. Don't do any loop-da-loops."

"Please," Shinji smirked, "I wouldn't want to damage the load." He said, and Toji shook his head and opened the back hatch of the cockpit.

Shinji watched him leave and close the hatch behind him, and as he turned he wasn't alone in the cockpit. In Toji's vacated seat was a young girl with pale skin, light blue hair and crimson eyes, wearing a blue and white school uniform.

"Ayanami?" Shinji blinked in surprise.

"In one year Humanity will end, Shinji," She said, turning her crimson eyes to him. "You and Pilot Sohryu will decide the fates. I am waiting for you, Shinji. But please, do not let them use our gifts as a weapon."

Shinji shook his head staring at the clone. "I don't understand, what are you talking about? You're dead… how… where are you waiting for me? What gifts? Is there going to be another Impact?"

"Yes," Ayanami began to fade, "its effects on Humanity will be yours and Pilot Sohryu's to decide."

Shinji gapped as the girl disappeared. He sat there for a moment before rubbing his face. "Shit…" He muttered to himself.

"You ok, Brother?" Toji asked as he reentered the cockpit.

"Toji… do you think Ayanami could have survived?" Shinji said, avoiding eye contact.

"You and your Eva ripped her and Tabris to pieces if memory serves," Toji said as he retook his seat, "Don't see how she could have made it, but then again, she was a resilient wall flower…" He gave his friend an odd look, "Weird dreams again?"

"Just… something popped in there," Shinji replied, tapping the side of his head.

Both young men's eyes widened when the Seagull jerked with an impact. "What was that?" Shinji asked, gripping the controls.

"We got trouble," Toji said, glancing out the window to see a group of dark colored aircraft fly past them. "Freight Pirates…"

"Haven't run into any of those for a while…" Shinji shook his head as he hit the throttle. "Seagull to any available aircraft! Mayday! We are being pursued by pirates. Request immediate assistance! Mayday! Mayday!"

"Take the stick," Shinji ordered, as he hit some switched bringing up the aircraft's defense guns controls.

"We don't have many rounds left, Shinji," Toji said, "Make every shot count, Shinji!"

While the fighters were more agile heavier armed, Shinji and Toji had the advantage that they didn't want to damage their supplies. Shinji closed one eye and focused his sights on one of their circling attackers. "Target locked, taking it out," Shinji growled as he pulled the triggers firing the aircraft's twin machine guns, and ate through the jet's wing armor. It exploded violently as it fell from the sky.

"One down, three to go!" Toji cheered, jerking the stick to dodge oncoming fire.

Shinji managed to get another in his sights and studied the fighter. "I think that one's the leader…" Shinji said, "Take it out and the others will probably bug out…"

"Then what are you waiting for?" Toji asked, moving the Seagull into firing position.

"Got the target… FIRING!" He pulled the trigger and only the sound of clicking echoed. "Oh crap."

"Should have splurged on ammo…" Toji closed his eyes, "Kensuke would kick our ass for this…"

"Don't worry," Shinji gulped, "I think these guys are going to do it for him…"

Shinji and Toji watched as the lead fighter turned and headed toward them, and then exploded violently. A new fighter flew through the exploding debris, this one far more advanced and painted completely red with the image of Evangelion Unit 02 painted upon the side of the jet. "It… can't be…"

"Civilian Transport," a very familiar voice with a German accent came through the radio. "This is Red Tiger Leader. We got your backs and going to escort you to T-4."

"C-Confirmed, As-Tiger Leader," Shinji replied, trying desperately to hide his voice. He failed.

"Ikari?!" Asuka Langley Sohryu's voice chimed back, sounding almost happy and excited. "Wow, I saved your ass… AGAIN! Just like old times!"

"Um… yeah, thanks, Asuka…" Shinji said awkwardly.

"You are VERY welcome, Third Child," the overtly confidant replied, taking position in front of the seagull. "Now be a good Baka, and follow me. And don't you dare try to run away from me again."

"Roger that," Shinji shook his head.

"I'm serious, Third," Asuka sounded honestly angry, "Even make me think you're going to break formation, I will blow your ass to smithereens! Red Tiger Leader out."

"I think she missed you," Toji smirked.

**NEON EXODUS YAMATO**

**Chapter 1: Rising like a Phoenix**

"How are the preparations, Captain?" the chairman of the barely functioning United Nations.

"Ship construction has been completed, Wave Motion Drive Engine has been tested and ready, and all weapon and defense systems are green. All we lack is loading enough food and water for our trip as well as getting the crew completely built up. I still lack my tactical officer and head pilot." The Captain replied.

"We don't have much time, just barely a couple days past a year before life on earth will be impossible," the chairman shook his head, "There are still many who do not trust you. And you cannot deny your hand in causing the Third Impact."

"I cannot, that's why this crew and I volunteered to do this," the Captain nodded, "We made this mess. We're cleaning it up."

"Very good, be ready to begin Operation Star Blazers as soon as you're fully prepared," the chairman nodded, "UN out."

"Hmm…" the Captain sat back in the captain's chair on the empty bridge and sighed loudly.

"Captain," a woman spoke over the com system.

"Report," the Captain said, glancing down at the blinking com light.

"Red Tigers are returning, Commander Sohryu said that she's bringing you a present," the woman replied.

"Oh boy… I'm on my way. Thanks, Maya," the Captain stood up and left the bridge.

-NEY-

"Keep close," Asuka instructed over the com as they flew over what was once the Pacific Ocean, still a few miles from where the Red Sea remained.

"We're not even headed toward Tokyo-4 anymore…" Toji said as Shinji maneuvered the Seagull behind Asuka's fighter.

The wing of aircrafts flew low and over what was once the ocean floor. "Would you look at that…" Toji said, and Shinji looked to see the wreckage of an old World War II battleship. "Kensuke would be going nuts if he saw that thing…"

"He'd love it," Shinji noted.

Asuka slowed down and Shinji backed off the throttle, and to the boys confusion twisted down into a canyon, on into a hidden cave. Once inside, the boys were surprised to see a fully furnished military complex. "Whoa…" Toji gapped, "Now this is awesome…"

"Transport Seagull, you are clear for landing on bay A-12," a woman's voice spoke through the com.

"That sounds like Ms. Ibuki…" Shinji blinked, before picking up the com mic. "Roger that, we're touching down eta two minutes…"

Shinji effortlessly brought his transport down to the landing pad, and the two boys walked down the gangplank. He blinked when he saw a beautiful young redhead in a red and yellow flight suit waiting for him with hands planted firmly on her hips.

"The Red Devil…" Toji recognized, then leaned over to Shinji and whispered, "She grew up nice…" his eyes admiring how the flight suit clung to her curves.

"Toji Suzuhara," She said power walking toward them. Then to Toji's terror, threw her arms around him in a friendly hug. "Good to see you aren't dead. Hikari would be sad… sorry how that worked out, too, by the way."

"Um… thanks… and good to see you too, Asuka…" Toji said awkwardly.

"And… You…" Asuka turned her eyes on Shinji with eyes of pure murder.

"Hey, Asuka, how have you been?" Shinji asked, and Asuka's skin flinched and twitched at the sound of his voice. He noticed she had a long, faded scar across her left eye, which contrasted her right ocean blue eye with an odd mix of green blue and red.

Before he could say anything else Asuka's clinched fist slammed into his chest just below his ribs. The air escaped his lungs, and as he tried to suck in another breath, her knee slammed up between his legs. He was finished off by a brutal upper cut that sent him spiraling to the ground. "YOU MISTSTUCK! She screamed as she towered over him, "DU HURENSOHN!"

"What was that for…" Shinji groaned, curling into a ball.

She stared at him in disbelief, "You have to ASK? Are you really that stupid? WHERE WERE YOU!? Not even a word! Not even a note! NOT A I HATE YOU, NOT A YOU SUCK, not even… a goodbye. You just took off in the middle of the night. And what? You expect me to just pull you in a hug, kiss your cheek, and tell you how much I missed you? FICK DICH, IKARI!" She yelled, then turned and stormed off.

"You ok, buddy?" Toji said, going down to one knee beside his friend.

"I… might… have had that coming…" Shinji groaned, forcing himself to a seated position.

"Look on the bright side," Toji patted his shoulder, "At least you know she hasn't changed much."

"Captain on Deck!" a dock worker called and everyone around stopped and stood at attention. Shinji and Toji glanced and spotted another familiar face, and much to Shinji's relief, Misato Katsuragi, dressed in a Captain's long coat and white and black navy captain's hat, looked happy to see him.

"Misato-san…" Shinji said as his old friend and former guardian walked toward him. "Please don't hit me…"

"What happened?" Misato asked as she offered him a hand.

"Asuka found me first…" Shinji groaned, accepting her hand. She flinched at the admission.

"In her defense, she did take your sudden disappearance rather hard…" She said as Shinji dusted himself off. Her eyes traveled across Shinji's body in a very un-parent-like way before she smiled at him. "You've grown up, Shinji." She said with a smile.

"Thanks, Misato…" He blinked in surprise when she pulled him into a warm hug.

"I've missed you, Shinji," She said, squeezing him slightly, "Welcome home."

"Where are we?" Shinji asked as they released one another. "What are you doing here?"

"I need to talk to you both about that actually," Misato said, "There was a purpose for your transport order beyond the shipment. Come with me and let's talk in private."

"I have a bad feeling about this, Chewie…" Toji whispered to Shinji.

Shinji scowled at his taller friend, "The hell I'm Chewie!"

Toji smiled and shook his head, "Who's the jerk with a heart of gold, and who's the straight man?"

Shinji blinked a moment before a look of disbelief and anguish crossed his features. "Shit… I _am_ Chewie…"

They walked into a small office and Misato closed the door behind them. "Have a seat, boys," Misato said motioning to the desk as she walked around to the other side of it.

"I'm certain you both have noticed with your transporting all over the world… the Earth isn't getting better," She said, pressing a button on a keyboard on her side of the desk. A moment later a holographic image of the Earth and the Moon appeared. The Moon was still soaked in Lilith's blood while the earth, where it was once a beautiful shade of blue and green with several white clouds was now dark red and brown with a few small patches of blue and green. "The truth is the Earth is dying."

"All studies show that in just a little over one year's time the Earth will not be able to support human life, and short while later, no life whatsoever," She said as the green and blue faded away leaving only red brown and black.

Toji and Shinji stared in shock, Shinji more so as he remembered the warning Rei had gave him just a short while earlier. "There has to be something we can do, Misato…" Shinji said, looking up at her.

"How much do you two know about your world history?" Misato asked, pressing a few buttons, "Particularly World War II?"

"Studied it in school, at least until the world ended," Toji replied, "Then survival and pilot training kinda took precedence…"

"I'm certain you saw the wreckage of the battleship above this base?" Misato asked, and the young men nodded. "During World War II, the Imperial Japanese Navy built the largest and most heavily armed warship to ever travel the seas: The _Yamato, _the flagship of the Japanese Combined Fleet. Unfortunately, she didn't see that many battles. Most notably she defended Japan during the Battle of the Philippine Sea, and went down fighting during Operation Ten-Go." She explained as video footage of the WWII era Warship was displayed before them. "We've been working at repairing and refitting her here."

"No offence, Katsuragi-san," Toji said looking at the seagoing warship, "But there's not that much water left. A battleship, especially a big battleship, isn't really that useful anymore…"

"Oh, it does more than float now," Misato said, smiling and glancing between the young men, "Alright, Toji, I expect this to be all Greek to you, but Shinji, how much do you know about the moons, the black moon and the white moon?"

"Where the Angels originated from… in according to my Father and Dr. Akagi's mother us too," Shinji nodded, frowning as he didn't want to go back to that part of his life. Ever. Again.

"The question is, where did they come from?" Misato pressed some buttons and the earth reappeared and began to zoom out. "This is the Milky Way, we are here," She said and a little flashing arrow with a smiley face appeared on the halo-projection, "After extensive research using Evangelion technology and… other things we have learned that they come from what has been dubbed the Ancestral Race. For reasons we do not know they launched the Seeds of Life, the White and Black Moon, out into space… we have reason to believe that they were not the only two either. If they created this… technology that would produce Instrumentality then… we… believe that they have the technology to undo it."

"There is a way…" Shinji said looking at his lap.

"Excuse me?" Misato looked surprised.

"Misato, fool me once shame on me," Shinji glanced up at her, "Don't forget, I was in NERV, too. You know more than you let on. Rei came to you, too, didn't she?"

Misato ducked her head a moment, "We did get some… surprise intelligence as well as advice on how to properly use technology derived from NERV's Evangelion technology. Particularly something called the Wave Motion Drive."

"We have learned that Iscandar is here," Misato continued, showing a galaxy a great distance away from Earth. "It is estimate one hundred and sixty eight thousand light years away from us."

"It takes a year and a half for one of our ships to reach Mars at top speed, Misato… We'd… our grandkids would arrive there and their great grandkids would be making it back home," Shinji blanched at the map.

"That's where the Wave Motion technology is so… COOL!" Misato beamed, hitting some buttons. "While I have no idea how it works myself, that's more Ritsuko and the engineers' department, it has the ability open temporary folds in space/time. If we do fold jump after fold jump, including cool down times, we can be there in a less than a year's time."

"So we take a ship that has this Wave thing on it, find these Ant Siesta Race guys, find out how to undo the Impacts' damage, then come back home?" Toji asked.

"Yup, it's a glorified grocery run," Misato nodded. "I assembled the crew, majority of them are members of NERV. We all had a hand in leading the world to this kind of shape. Where the majority had no idea and was manipulated by Commander Ikari, all of our hands are still bloody regardless the motive. They… we see it as a way to redeem ourselves for our involvement. We have two more spots on my bridge crew needing to be filled: Pilot and Tactical officer/gunner. We need you both. I need you. Shinji, Toji, what do you say? Wanna go on an adventure?" She added with a smile.

-NEY-

"I can't believe she talked us into this…" Toji complained as they walked down the hallway, Shinji looking at a map of the base that Misato had left, with hand drawn instructions to Medical.

"You always said you wanted to be a hero like the Eva Pilots…" Shinji pointed out.

"Yeah, and that bright idea had me crippled till Third Impact," Toji grumbled, then stiffened in realization. "Sorry, brother. I didn't mean…"

"It's ok, and besides it shouldn't be that bad," Shinji shrugged, "glorified grocery run."

"We'll see," Toji said, and Shinji looked up at the Red Cross sign, "Here we are."

Toji opened the door and they walked into the med bay. A young brunette nurse turned and looked at them. Toji and the girl's eyes met, and Toji gapped and the girl smiled happily. "Onii-san, Shinji-kun, great to see you!"

"Sakura? What are you doing here?" Toji asked his younger sister.

"I'm one of Dr. Sado's RNs," Sakura Suzuhara replied, pulling out a blue rubber glove. "Captain Katsuragi gave us a heads up that you were coming. Now both of you… Drop your pants." She said, snapping a rubber glove on.

"Beg your pardon?" Toji asked while Shinji turned beat red.

"Drop. Your. Pants." She said slowly as if speaking to a child as she pulled a tray around.

"Why?" Shinji croaked, "If you don't mind us asking…"

"Couple reasons," She said, holding up a syringe, "Vaccination to the butt," And she held up a variety of probes and elongated Q-tips. "We have to test for any possible infections and diseases… all openings I'm afraid. Don't worry…" An almost sinister and predatory look crossed the young nurse's features. "I'll be gentle…"

-NEY-

_**Mars Base**_

"You're almost out of fuel, Kodai-kun," a blond headed woman in a yellow uniform said through the com from the command tower of the former SEELE now UN base on the surface of Mars.

"Have to make sure the asteroids are clear for the ship's course, Yuki-chan," the pilot of the shuttle said to his wife as he flew among the rocky debris.

"Going on a deep space mission to save all of humanity," Yuki said, somewhat dreamily, "It'd be amazing... Do think we'll ever have an opportunity like that, Kodai?"

"Maybe in another life," Kodai replied, doing a loop in his shuttle. "Never know, you might even be an ace-pilot!"

"I'm not that bad…" Yuki pouted. She blinked as the radar began to bleep in front of her. "Kodai, something's wrong…"

"I'm seeing it too, Yuki. As soon as I'm in and the landing bay is sealed, head toward the bunker…" He said, seeing the large beeps surrounded by hundreds of other beeps approaching from the opposite side of Mars from Earth.

"Kodai, please be careful… hurry to me." She said, as she forced her hands to not tremble as she readied the base automated defenses and ordered an evac to the Anti-Angel bunkers.

"I'm on the way in," He said punching the throttle, "This is Commander Susumu Kodai of Mars Base, we have multiple UFOs approaching from unknown space, request assistance."

"They're never going to make it…" Yuki said softly.

"Someone will… hang on, Yuki-chan… I love you…" Kodai said as he brought his shuttle in, praying for a miracle.

-NEY-

**Battleship Yamato Site**

"Who are they?" Misato frowned from her ready room, looking at the transmitted information from Mars Base.

"Unknown," the UN admiral replied, "Mars Base has limited defense, and the personnel have been moved to underground Anti-Angel bunkers. Project Star Blazer's Warp Drive can get you there in time to save them on the way the mission. It is on the course path outside of the galaxy… it just seems you'll have to leave earlier than expected. Are you prepared?"

"Yes but I was hoping for more system tests before we leave the planet…" Misato frowned. She sighed and sat back in her chair, "Well, we wondered if there was any other life besides us… this can't be a coincidence that as the LCL is close becoming its purest on Earth that these guys show up seemingly on the way here?"

"It's not unlikely that they could be LCL scavengers," the admiral replied.

"ET Ambulance chasers…" Misato shook his head, "We'll take off as soon as everyone's on board and at their stations. Katsuragi out." She said with a nod.

"God's speed, Katsuragi." The UN admiral replied as the screen turned off.

Misato took a deep breath and lifted her mic. "All hands, this is the Captain speaking. We have an emergency situation at Mars Station. We will lift off immediately and go to rescue the Mars Base staff. I know we expected one more night on earth to rest and prepare but that's just how the dice rolls. All hands battle stations. Primary Bridge Personnel to First Bridge, we've been preparing for this, people. It's time to show them what we're made of."

She released the call button, and sat it down. A moment later the alert siren sounded and she pressed a couple buttons on her chair, and it lowered through the floor toward the First Bridge.

Shinji and Toji ran down the hallway and Asuka turned a corner almost plowing into Shinji.

"Watch where you're going you… Baka?!" Asuka blanched.

"That's Commander Baka now," Shinji replied, "Get the Red Tigers in their cockpits and on standby,"

"Wha… who the hell do you think you are? Do you honestly think you can tell me what to do?!" Asuka's face turned blood red with anger.

"Misato made me Tactical Officer," Shinji said matter-of-factly, "So that's who the hell I think I am."

Asuka blinked several times before glaring, "Ok, fine. But I sure as hell am not going to salute you!"

They parted ways and Shinji and Toji arrived at the elevator that took them to the bridge. They walked off to the advanced space-cruiser-like bridge lay out.

"Welcome to the bridge, gentlemen," Misato said, fully into her old NERV Commander mode. "Shinji take the gunner position, Toji, take the helm." Shinji sat in the center of the ship while Toji sat to the far right.

The boys gave a quick salute and took their positions. Misato picked up a mic. "Chief Aida, are we ready to go?"

"Wave Motion Drive online and charged, waiting for the command to connect the fly wheels, Sir!" the familiar voice spoke through the con, causing Shinji and Toji to look at each other in surprise.

"Do it, Chief," She looked forward, "All hands prepare for lift off. Open the windows."

Shinji and Toji covered their eyes as an outer layer over the forward glass broke away, showing that they were in the command tower of the one sunken wreckage.

"Wait, we're flying into space in a sunken chunk of scrap?" Toji asked.

"That was just camouflage for the repair and star cruiser upgrades," the ship's AI, Analyzer, replied through the consoles.

"All systems ready to launch," Maya Ibuki announced from her station on the left of the bridge.

"Alright…" Misato nodded and sat back. "**YAMATO HASSHIN!**"

The buried engines screamed as the ground trembled from the force of the mighty warship began to rise through the rocky ground. The fake rusty metal broke away showing shimmering new alloy metal armor. The long warship had one large thruster and two smaller ones below it at the rear, a large central tower with two bridges and the captain's cabin at the top, and a missile tower attached to the back of it, had two large three cannon guns on the rear and three on the front, and multiple twin cannons along the center sides, and at the very bottom of the ship's hull was a third bridge. Finally an odd port was closed at the very tip of the ship. From the ashes of the WWII Battleship Yamato, the Space Battleship Yamato had risen.

"All systems running optimally," Ritsuko reported from the third bridge. "We are ready to activate warp system as soon as we pass the moon's orbit."

"Good. Steady as she goes, Mr. Suzuhara," Misato said as they rose higher and higher into the sky. "Hang on, Mars. Help is on the way…"

_Uchuu Senkan Yamato!_

_Farewell, Earth!_  
_The ship that is departing is_  
_The Space Battleship Yamato!_

_It departs now to Iscandar_

_At the end of the cosmos, bearing its fate_  
_"We will come back, no matter what it takes,"_  
_Answer with a smile to the waving people!_

_Going far from the galaxy toward Iscandar_  
_A faint gleam of hope_  
_The Space Battleship Yamato!_

_Farewell, Earth! Farewell, beloved ones!_  
_The Space Battleship Yamato!_  
_Bearing the fate of saviors of Earth_  
_The men fight and the romance burns high_  
_Somebody has got to do this_  
_We are the people they count on…_

_Going far from the galaxy toward Iscandar_  
_A faint gleam of hope_  
_The Space Battleship Yamato!_

_The Space Battleship Yamato!_

**TO BE CONTINUED… **

**Next chapter: The Yamato's maiden flight faces a new threat. What secrets do these aliens hold? What secrets does the Yamato itself hold? Questions will be answered and questioned will be asked… as well as a good dose of fanservice! Neon Exodus Yamato chapter 2… coming soon! **

**Song credit: "Space Battleship Yamato" main theme (English translation) **


	2. Chapter 2

"_**The Universe, so far as we can observe it, is a wonderful and immense engine; its extent, its order, its beauty, its cruelty, makes it alike impressive" **_**– George Santayana - 1916**

_One Week after Third Impact… In the Ruins of Tokyo 3_

Shinji Ikari slowly limbed up the broken blood stained steps of the NERV apartment complex that they had once called home, and now simply call shelter. He opened the unlocked door and smiled when he saw the red hair seated on the couch of the living area. "I'm back, Asuka," Shinji said fumbling with the bag in his arm. "I found some more cans; we'll be eating well tonight."

Asuka glanced away from the blank screen of the TV to look at Shinji with her uncovered eye. "Can food's disgusting…" She said with a frown, "Even the Not-So-Invincible Shinji can make that crap taste good."

"There's been some more people rise from the Sea," Shinji mentioned as he started to put the cans away. "Finally getting some people we know. Kensuke was among the risers. Hikari and I both were happy to see him, bet Toji will be back soon too."

"Whatever…" Asuka said with little interest.

Shinji frowned and glanced down, "Hikari asked if you'd want to help out once you're feeling better…" Asuka shrugged, "I'm just happy people are coming back, aren't you, Asuka? Never know, Misato-san could be coming back soon, too. Maybe even Kaji…"

"You really are stupid!" Asuka shouted, pounding the arm of the couch with her good arm, "Kaji was dead before you screwed up this planet, Ikari," Asuka spat, standing and turning toward him. "And Misato died before it, too. They're gone, and I'm stuck with YOU!"

"I'm…" Shinji started to say as he stared at his feet.

"Don't you dare, don't you freakin' dare apologize!" Asuka stormed toward him, "Apologizing doesn't bring Misato and Kaji back! It doesn't bring back my mother, but knowing you, the all mighty savior Shinji will get his mommy back sometime!"

"Asuka, I know I just…" Shinji shuffled his feet, "I don't know what…"

Asuka growled and lifted her hand to slap him, when the door swung open. Both faces turned to see who had interrupted the German's latest tantrum. "Misato?" The croaked in unison.

In the door way, wearing only a thin coat of LCL, and rubbing her eyes and temples, "I don't know what the hell happened but… I feel like my head was blown off my shoulders…"

Shinji sniffled just a moment before he ran toward her, hugging her tightly. "Misato! You came back! You came back!" He cried, hugging her tight, and she returned it gently, still confused but welcoming him anyway.

Asuka stared at the two for a moment, before a tear slid from her uncovered eye, and she ran toward them as well, throwing her arms around Shinji's shoulder and around Misato's back, burying her face in Misato's bare shoulder.

The three held each other tightly for several moments, crying happily. Finally Asuka turned her face toward Shinji and smiled darkly. "Hey, Shinji-kun, you're hugging Misato."

"I think I figured that out, Asuka…" Shinji frowned, turning his eyes to look at her.

"She's naked, Shinji…" Asuka grinned at his sudden horrified expression.

Shinji jumped back, stammering various words without forming a single sentence as he moved quickly away while covering his eyes.

"You had to bust up the moment, didn't you, Asuka," Misato glanced to the young redhead. "I was hoping he'd notice a nipple or 'accidently' cop a feel of my magnificent backside first…" Misato sent Shinji an impish smile. Shinji released a cry of shock, before he tossed her shorts and tank top at her face.

"GET UN-NAKED!" Shinji yelled, hiding his eyes.

"Wow…" Asuka stepped back, trying to make a look of disgust, but couldn't remove the smile from her lips. "I don't know who's the bigger pervert, Misato… you or him…"

Once Misato was dressed, Shinji went to work in the kitchen, making the best meal he could come up with, asking a barrage of questions toward Misato, how she felt, if she was hungry, thirsty, tired, etc.

Misato sat at the table with Asuka, as Asuka rambled about what she had missed since Third Impact. Shinji piped in every so often, which often led to a much more good natured argument. A smile crossed his face, for the first time since they had returned, he felt at home. He felt as if he was a part of and with family. He felt nothing could happen to them anymore. He felt that the worst was behind them…

He was wrong.

**NEON EXODUS YAMATO**

**Chapter 2: The Power of Wave Motion**

_**Present Day… **_

"We will be leaving Earth orbit in forty Five seconds," Maya reported from her station.

"Prepare to close the glide wings," Misato ordered from the captain's station, her arms crossed as she watched the actions on the bridge as well as the gauges. "How's she handling, Mr. Suzuhara?"

"Smooth, VERY Smooth," Toji replied shifting the control wheel and stick slightly to keep the Yamato flying straight. "She's got a hell of a lot of power pushing her."

She studied the readouts and saw that they'd be facing the old NERV moon base. "Let's give the Moon Base a fly by, they're the ones that constructed the Wave Motion Drive and the Yamato's engines," Misato nodded toward the blood-stained moon. "Let's let them see the fruits of their labors."

The battleship broke orbit of earth and its three thrusters roared, glowing a bright golden yellow as it pushed farther into space.

The bridge was silent as they approached the moon except for the beeping of instruments. A small smile crossed Misato's face as she leaned back into her seat. "Fly me to the moon," She sang softly but loud enough to perk everyone's ears. "And let me play among the stars…"

"Won't you let me see what spring is like on Jupiter and Mars," Maya added in with her.

"In other words, hold my hand," other bridge crew began to join in, "In other words, Darling, kiss me."

"Fill my heart with song, and let me sing forever more," Toji added in, surprising everyone with the best singing voice on the bridge, earning a quirked eyebrow from Shinji. "You are all long for, all I worship, and adore,"

Shinji shook his head before joining in completing the bridge crew in song. "In other words, please be true…"

"In other words… I love you." They finished with laughter.

"Good stuff," Misato shook her head with a smile. "Very impressive, Suzuhara," she noted, causing a blush to cross the pilot's nose.

"Since when did you learn to sing?" Shinji glanced at his friend.

"I have many secrets," Toji stuck out his chest, "I could teach NERV and SEELE a thing or two."

"Captain, Moon Base is hailing us," Maya spoke up.

"On the main screen," Misato ordered, and a group of scientists appeared on the large monitor above the forward windows of the bridge. "Hello, Gentlemen. Greetings from the Yamato."

"Captain Katsuragi," the lead scientist greeted, "She's… beautiful."

"Speaking of the ship or her captain, gentlemen," Misato gave a playful wink.

"Both…" the flushing scientist replied.

"Good answer," Misato nodded, "We're about to engage the Wave Motion Drive, any last minute advice before we warp?"

"All reports say you are good to go, Captain," the lead scientist replied.

"How's this work anyway?" Toji asked as he manned the controls.

"It's an odd mix of complexity and simplicity actually," the scientist replied, "Through information gained from the Advisor, we've learned that the dimensions, such as our own isn't actually a flat plane, instead it's more like sharp waves made of tachyon energy. Normally as you travel along you move in sync with the tachyon waves, smoothly going up and over and down, no problems." He took a moment to make sure they were following him. "When the Wave Motion Drive is activated, it uses draws power from tachyon waves and uses them to push the Yamato out of sync, and it will allow it to punch through the space-time, moving far beyond the speed of light."

Toji glanced to Shinji, and then nodded toward the scientist on the monitor. "_Magic_, got it." Toji stated with a thumbs-up, and Shinji face-palmed.

"Alright then, are we ready to give this thing a shot?" Misato asked glancing around the crew.

"One warning, make sure you hit the timing just right…" the scientist advised, "You don't want to come out in the middle of an asteroid, planet or star… or worse case… miss the other end completely."

"Where would we end up?" Maya asked, a hint of nervousness in her tone.

"We… don't know," The scientist shrugged, "It might be best not finding out."

"Good advice…" Misato sat back and crossed her legs. "Ok, Engineering… engage Wave Motion Drive," She ordered on her microphone. Engineering replied and the ship engines shut down for a moment before a distinct roaring began to echo throughout the ship as the Wave Motion Drive came online. "Mr. Suzuhara, punch it."

"Aye-aye, Captain," Toji replied, pushing the throttle. The Yamato pushed forward as a long blue burst of swirling energy trailed behind it from the main thruster.

"Prepare to jump on my mark," Misato ordered as space itself began to ripple around the ship. "Five… Four… Three… Two… One… JUMP!" And in a flash the Planet Mars appeared directly in front of them.

"Whoa…" Shinji breathed as the crew gasped at the lurching stop.

-NEY-

On board the massive carrier ship over the Planet Mars, a crew of blue skinned human-like aliens stood upon the bridge as their drone warships attacked the Terran base. "Commander, we've detected another ship, as well as Wave Jump signature."

"Why would Lord Desler send another ship?" the commander narrowed his eyes.

"This isn't one of our ships, Sir," the crewman responded, "It warped from the direction of the Planet Terra."

"Very curious…" the commander rubbed his chin, "More survivors of Instrumentality? It's unheard of… And how could these barbarians have warp technology?"

"Orders, sir?"

"Ignore the Terran base, and focus on this ship. Destroy it then bring the pieces on board to examine."

-NEY-

"We got incoming," Maya replied, "They're coming in hot."

"Introduce them to our main batteries," Misato ordered, "activate missile and pulse laser defenses."

"Yes, ma'am," Shinji nodded hitting some keys and speaking into his radio. "Shock Cannon Battery One, Two, and Three target incoming ships and fire at will. Prepare side missiles and pulse lasers to fire at any that make it past initial barrage."

The three gun towers at the front of the Yamato lifted each three barrel set and fired heavy beams of energy at the incoming ships, ripping through them as if they were made of plastic. What few made it past were easily destroyed by the side missile launches and walls of pulse lasers along the side of the ship. "First wave neutralized, Captain." Shinji reported.

Onboard the mothership the commander nodded in appreciation. "The unidentified warship has some teeth it seems… send in all fighters along with all remaining warships."

Back on the Yamato, Maya reported the next wave coming. "Launch the fighters," Misato ordered.

Shinji nodded at the order, and lifted his microphone, "Red Tigers, launch and attack incoming ships." Shinji hesitated a moment, "Hey, Asuka."

"What is it, Commander Baka?" Asuka's annoyed voice replied.

"Give them hell," Shinji smiled.

"Please, like I was going to give them anything else, dummy," She replied, as her fighter hit the air along with her squadron.

The fighters along with the Yamato's heavy weapon systems held fast, but they weren't making any progress. The crew gasped as a single fighter, damaged from Shinji's Shock Cannon barrage spun out of control straight toward the First Bridge. Before anyone could do anything it exploded violently and Asuka's fighter made a close flyby. "Hey, Commander Baka? I'm thinking of keeping a score on my fighter of the times I save your ass. Probably get a larger count than even my impressive kill count. What do ya think?"

Shinji just smirked then gasped when an explosion hit close to the ship.

"This is getting to close," Misato frowned as she oversaw the battle. "Shinji, order all fighters to clear from the forward of the ship. Toji, line us up with the enemy command ship. We're going to put a stop to this, right now."

Shinji and Toji did as told, and the Yamato turned to face the enemy. Ritzuko's face suddenly appeared on a window of the main monitor from where she was stationed in the Third Bridge. "Misato, the Gun hasn't ever been tested! This thing could backfire and blow us all the way back to earth… IN PIECES!"

"If we don't these guys will pick us apart till we're pieces…" Misato shook her head, and then made the order, "Ready the Wave Motion Gun!"

"The what?" Shinji asked as Misato triggered an alarm.

"See that covered switch on the side of your console? Open it up, and hit that red button." Misato pointed, and Shinji did as instructed. After he hit the button, the top of his console opened and what looked like a hand gun on a joystick and a small powered down targeting screen rose before him. "Alright, Shinji, with that pistol you have full control of the ship. Activate the target scope, get a target lock, but don't pull the trigger until I tell you. When you're ready tell Engineering to deactivate the safeties."

Shinji did as told, and wrapped his hand around the handle of the pistol. A twirling targeting system appeared on the HUD screen before him, and as he twisted the handle, the maneuvering rockets moved the ship in time with it. A shrilling beep sounded that he had a lock. He picked up his command mic and brought it to his face as he maneuvered the ship with the pistol "Target Scope open, Engineering, deactivate safeties." He said as he brought the mothership into the center of the scope.

"Safeties unlocked. Wave Motion Drive at 90% power and charging," Chief Engineer Aida reported. "100% charge…"

"Wait for it…" Misato leaned forward.

"105%... 110%...115%... 120% we're maxed out, Captain."

"Fire at will, Shinji," Misato ordered, "All hands, brace for Flare and Recoil!"

Shinji and everyone else on the bridge pulled out dark goggles and placed them over their eyes. "Firing in Five… Four… Three…" Shinji counted down, focusing on the target, an odd feeling filling his stomach. Rei's words about not using "it" as a weapon returned to his mind. Was this what she was talking about? Should he refuse Misato's order? If he doesn't, they'll all be killed and any hope for earth will be lost.

"Shinji, fire! We're out of time!" Misato called as the attack warships were closing in. "Two, one! Fire…" Shinji pulled the trigger. And for a fraction of a second nothing happened. Then a hum began sound from the front of the ship, that grew louder and louder till finally a massive pillar of light erupted from the opening at the front of the Yamato. The warships, most of the fighters, and the command ship were completely engulfed in the massive beam of destruction, leaving nothing to even explode. What enemy ships dodged the actual beam was forced to explode just from the tachyon energy radiating from the beam.

"Holy shit…" Asuka breathed as her fighter team gapped at the powerful blast. She never even saw the chunk of broken, burning steel spinning down toward her from above.

"Majority of the enemy was destroyed, three warships escaped and are regrouping," Maya reported.

"How soon can we warp out?" Misato asked.

"Ten Minutes for a recharge enough to take a jump," Aida replied.

"Shinji recall the fighters," Misato ordered, "Maya, send a message to Mars base to power down all electronics. We're going to jump out and fire off a short range EMP mine to finish off those three. Just gotta draw them in close. Get ready to move, people!"

Shinji nodded, "Red Tigers, return to base. Excellent job."

Shinji watched his readouts as each of the ships were electronically checked back in as they docked in the rear fighter hatch of the ship, just below the engines. All but one ship checked, "We're missing Tiger Leader, Maya?"

"I'm picking her up on radar… she's not moving." Shinji's eyes widened at Maya's report.

"How much time till we jump?" Shinji asked.

"We have seven minutes…" Misato frowned, "Hurry, and bring her home, Shinji."

Shinji nodded and started for the door. "If you don't make it, power down when the EMP fires, then try to land at Mars base."

"We'll make it back," Shinji stated, before running out the door.

-NEY-

"Damnit… Damnit…" Asuka whispered softly as she tried again to restart her fighter's engine. It was dead in the water, and she was fighting down panic as she saw her Oxygen levels dropping below 10%. Still wasn't as bad as the last time she died. Suffocation was slightly better than being stabbed to death then ripped apart by smiling, winged, demonic Evangelions. Just slightly. Was this why she had a second chance at life? To die out here in space? This wasn't in her plan. Not much of this was, anyway.

Baka-Shinji had come back into her life, and there was still so much she wanted to say to him, after she was finished being angry at him, then hitting him a few times. So much undone and unsaid. Tears formed in the corners of her eyes. Maybe, she should have hugged him, kissed his cheek, and let him know she missed him when they met on that dock bay, seeing as kicking his ass again didn't have the same feel-good effect it used to have.

"Shinji…" glanced up the battleship Yamato in the distance, thinking back at the time she was falling into hopeless doom in that volcano. But there was no Invincible Shinji and his Evangelion Unit 01 to pull her back from the brink this time. It was over. "Goodbye, Shinji…" She forced through difficult breath, "I…"

"Need a lift, Asuka?" Her eyes widened in shock at the radio message.

"Shinji?" Asuka sat up in surprise.

"Does your ejection system still work, Asuka?" Shinji asked, and she glanced to see a green and purple fighter approaching rapidly.

"Go back to the ship, Shinji, you don't have time to get me," Asuka said in reply.

"Have you forgotten I'm Commander Baka? I give the orders!" Shinji asked, "Now answer the question, Pilot, can you eject."

"Yes, I can eject…" She said, beginning to struggle to breath, and she saw the oxygen level was at 1%.

"Then get out of there, Asuka, I'll catch you," Shinji replied, "Let's get out of here."

Asuka reached down and found the lever under her seat, and jerked it. Immediately the canopy of her fighter flew off, and she was thrown into space. Shinji's fighter Cosmo Zero One swooped in, and a pair of mechanical arms extended from the bottom and gently grabbed and pulled Asuka's space suit close to the fighter. Shinji turned the fighter quickly and rocketed back toward the ship. He saw the waves beginning to form around the ship and knew it was close to jumping, and the three warships were approaching it quickly. "Hang on, Asuka, we are going to make it!" Shinji pushed the throttle and aimed toward the open back hatch of the Yamato.

He barely dodged the launching of the EMP mine and landed just as the ship made its jump.

The EMP mine exploded sending out an anti-electronic wave. The three enemy ships were caught in helpless against the EMP wave. They instantly lost all power and slammed into each other, exploding violently.

"Did they make it?" Misato asked with concern.

"Cosmo Zero One landed just in time…" Maya reported, everyone on edge, "And he has her!" the applause rang out on the bridge, as Misato sat back roughly, pulling her hat over her eyes.

"I'm getting too old for this, you two…" Misato groaned toward Shinji and Asuka.

-NEY-

On Mars Base, Kodai and Yuki watched the battle, Yuki slightly amused as Kodai stared at the Yamato like a child watching a cartoon. "I would love to command a ship like that…" Kodai breathed with a smile.

"Maybe you will," Yuki replied with a playful smile. Kodai gave her a curious, hopeful look, "In another life anyway." She said cheekily, earning a shove from her husband.

"Hush and help me bring our systems back online," He grumbled going back to work.

-NEY-

In the Yamato's hanger bay, Shinji jumped from the Cosmo Zero One's cockpit and moved to help Asuka from the ship's arms. He was filled with concern as he lowered her down and realized she was lying limp.

"Asuka?" He asked, pulling off her helmet, and listened for breath. His eyes widened in terror as he felt nothing. "Oh no, you don't…" He said pulling open her flight suit, exposing her pink bra. Not even bothering thinking about it, he began chest compressions, "Don't you dare die on me, Asuka…" He said, pushing on her chest, and then lowering down to do mouth to mouth.

One of Asuka's pilots yelled for them to call the medics, but Shinji didn't even offer them a glance. He was completely focused on the redhead laying before him. "C'mon, Asuka, don't leave us…" He said, moving in for another breath of life, "don't leave me…" He breathed again, and rose back when she gasped into his mouth. "Asuka?"

"Mein Gott, Baka-Shinji…" Asuka breathed hoarsely, her blue eyes glanced to him, barely focused, "after all these years… your kissing still sucks… pervert…"

Dr. Sado and Sakura arrived a moment later, and Shinji helped them load her on a stretcher. Shinji reluctantly let go of Asuka's hand as they rolled her away, and he glanced down at it. He hadn't even realized he took her hand in his. He released a deep breath of relief knowing they had made it.

He glanced up to see them rolling her toward the elevator. He felt a longing to follow, to stay by her side. He glanced back down to the gloved hand that had instinctively clung to Asuka's. He needed to be by her side, and a part of him felt she needed him to be there, too.

Shinji turned and walked in the other direction with his head lowered. "I guess as much has changed… some things stay the same…" He whispered to himself…

…as he ran away from her again.

**To Be Continued…**

**Not too crazy with how I ended this chapter, it was actually a bit longer, but felt it was getting a bit too long and drawn out so I split it here. Next chapter a few more old friends will make their presence known on the Space Battleship, as well as more detail on how Shinji and Misato and Asuka parted ways. And don't forget more fanservice ;) more to come!**


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